Characterisation of the mating-type loci in species of Elsinoe causing scab diseases

The genus Elsinoe includes many aggressive plant pathogens that infect various economically important agricultural, horticultural and forestry plants. Significant diseases include citrus scab caused by E. fawcettii and E. australis, grapevine spot anthracnose by E. ampelina, and the emerging Eucalyptus scab and shoot malformation disease caused by the recently described E. necatrix. Despite their importance as plant pathogens, little is known regarding the biology of many Elsinoe spp. To gain insights into the reproductive biology of these fungi, we characterized the mating-type loci of seven species using whole genome sequence data. Results showed that the MAT1 locus organization and its flanking genes is relatively conserved in most cases. All seven species manifested a typical heterothallic mating system characterized by having either the MAT1-1 or MAT1-2 idiomorph present in an isolate. These idiomorphs were defined by the MAT1-1-1 or the MAT1-2-1 gene, respectively. A unique MAT1-1 idiomorph containing a truncated MAT1-2-1 gene, and a MAT1-1-1 gene, was identified in E. necatrix and E. fawcettii genomes. Additionally, two idiomorph-specific proteins were found in the MAT1-1 and MAT1-2 idiomorphs of E. australis. Universal mating-type markers confirmed heterothallism across 21 Elsinoe spp., are poised to advance future studies regarding the biology of these fungi.

The increasing threat to European forests from the invasive foliar pine pathogen, Lecanosticta acicola

European forests are threatened by increasing numbers of invasive pests and pathogens. Over the past century, Lecanosticta acicola, a foliar pathogen predominantly of Pinus spp., has expanded its range globally, and is increasing in impact. Lecanosticta acicola causes brown spot needle blight, resulting in premature defoliation, reduced growth, and mortality in some hosts. Originating from southern regions of North American, it devastated forests in the USA's southern states in the early twentieth century, and in 1942 was discovered in Spain. Derived from Euphresco project 'Brownspotrisk,' this study aimed to establish the current distribution of Lecanosticta species, and assess the risks of L. acicola to European forests. Pathogen reports from the literature, and new/ unpublished survey data were combined into an open-access geo-database (http://www.portalofforestpathology.com), and used to visualise the pathogen's range, infer its climatic tolerance, and update its host range. Lecanosticta species have now been recorded in 44 countries, mostly in the northern hemisphere. The type species, L. acicola, has increased its range in recent years, and is present in 24 out of the 26 European countries where data were available. Other species of Lecanosticta are largely restricted to Mexico and Central America, and recently Colombia. The geo-database records demonstrate that L. acicola tolerates a wide range of climates across the northern hemisphere, and indicate its potential to colonise Pinus spp. forests across large swathes of the Europe. Preliminary analyses suggest L. acicola could affect 62% of global Pinus species area by the end of this century, under climate change predictions. Although its host range appears slightly narrower than the similar Dothistroma species, Lecanosticta species were recorded on 70 host taxa, mostly Pinus spp., but including, Cedrus and Picea spp. Twenty-three, including species of critical ecological, environmental and economic significance in Europe, are highly susceptible to L. acicola, suffering heavy defoliation and sometimes mortality. Variation in apparent susceptibility between reports could reflect variation between regions in the hosts' genetic make-up, but could also reflect the significant variation in L. acicola populations and lineages found across Europe. This study served to highlight significant gaps in our understanding of the pathogen's behaviour. Lecanosticta acicola has recently been downgraded from an A1 quarantine pest to a regulated non quarantine pathogen, and is now widely distributed across Europe. With a need to consider disease management, this study also explored global BSNB strategies, and used Case Studies to summarise the tactics employed to date in Europe.

Ethnicity and the surgical management of early invasive breast cancer in over 164 000 women

Background

Limited information is available about patterns of surgical management of early breast cancer by ethnicity of women in England, and any potential inequalities in the treatment received for breast cancer.

Methods

National Cancer Registration and Analysis Service data for women diagnosed with early invasive breast cancer (ICD–10 C50) during 2012–2017 were analysed. Multivariable logistic regression was used to estimate odds ratios (ORs) and 95 per cent confidence intervals for the risk of mastectomy versus breast‐conserving surgery by ethnicity (black African, black Caribbean, Indian, Pakistani and white), adjusting for age, region, deprivation, year of diagnosis, co‐morbidity and stage at diagnosis.

Results

Data from 164 143 women were included in the analysis. The proportion of women undergoing mastectomy fell by approximately 5 per cent between 2012 and 2017 across all the ethnic groups examined. In unadjusted analyses, each ethnic minority group had a significantly higher odds of mastectomy than white women; however, in the fully adjusted model, there were no significantly increased odds of having mastectomy for women of any ethnic minority group examined. For example, compared with white women, the unadjusted and fully adjusted ORs for mastectomy were 1·14 (95 per cent c.i. 1·05 to 1·20) and 1·04 (0·96 to 1·14) respectively for Indian women, and 1·45 (1·30 to 1·62) and 1·00 (0·89 to 1·13) for black African women. This attenuation in OR by ethnicity was largely due to adjustment for age and stage.

Conclusion

Allowing for different patterns of age and stage at presentation, the surgical management of early breast cancer is similar in all women, regardless of ethnicity.

Epitypification of Ceratocystis fimbriata

Ceratocystis accommodates many important pathogens of agricultural crops and woody plants. Ceratocystis fimbriata, the type species of the genus is based on a type that is unsuitable for a precise application and interpretation of the species. This is because no culture or DNA data exist for the type specimen. The aim of this study was to select a reference specimen that can serve to stabilize the name of this important fungus. We selected a strain, CBS 114723, isolated from sweet potato in North Carolina, USA, in 1998 for this purpose. The strain was selected based on the availability of a living culture in a public depository. A draft genome sequence is also available for this strain. Its morphological characteristics were studied and compared with the existing and unsuitable type specimen as well as with the original descriptions of C. fimbriata. The selected strain fits the existing concept of the species fully and we have consequently designated it as an epitype to serve as a reference specimen for C. fimbriata.

Disability and participation in breast and bowel cancer screening in England: a large prospective study

BACKGROUND

There is limited information about participation in organised population-wide screening programmes by people with disabilities.

METHODS

Data from the National Health Service routine screening programmes in England were linked to information on disability reported by the Million Women Study cohort participants.

RESULTS

Of the 473 185 women offered routine breast or bowel cancer screening, 23% reported some disability. Women with disabilities were less likely than other women to participate in breast cancer screening (RR=0.64, 95% CI: 0.62-0.65) and in bowel cancer screening (RR=0.75, 0.73-0.76). Difficulties with self-care or vision were associated with the greatest reduction in screening participation.

CONCLUSION

Participation in routine cancer screening programmes in England is reduced in people with disabilities and participation varies by type of disability.

Genera of phytopathogenic fungi: GOPHY 1

Genera of Phytopathogenic Fungi (GOPHY) is introduced as a new series of publications in order to provide a stable platform for the taxonomy of phytopathogenic fungi. This first paper focuses on 21 genera of phytopathogenic fungi: Bipolaris, Boeremia, Calonectria, Ceratocystis, Cladosporium, Colletotrichum, Coniella, Curvularia, Monilinia, Neofabraea, Neofusicoccum, Pilidium, Pleiochaeta, Plenodomus, Protostegia, Pseudopyricularia, Puccinia, Saccharata, Thyrostroma, Venturia and Wilsonomyces. For each genus, a morphological description and information about its pathology, distribution, hosts and disease symptoms are provided. In addition, this information is linked to primary and secondary DNA barcodes of the presently accepted species, and relevant literature. Moreover, several novelties are introduced, i.e. new genera, species and combinations, and neo-, lecto- and epitypes designated to provide a stable taxonomy. This first paper includes one new genus, 26 new species, ten new combinations, and four typifications of older names.

Abstract P6-10-15: Lifelong vegetarianism and breast cancer risk in India: A multicentre case control study of 2101 women

Background

Breast cancer is now the most commonly diagnosed malignancy in women in India with over 150,000 incident cases per year. Interest in the role of diet in the aetiology of breast cancer is stimulated by the observation of the lower incidence of breast cancer in Asian populations where the intake of animal products is lower than that of Western populations. Studies investigating this relationship to date in India have been of small size and provided conflicting results and therefore a large scale case-control study in India addressing this relationship is of interest.

Methods

Between 2011 and 2014 we conducted a multicentre hospital based case-control study in eight cancer centres in India. Eligible cases included women aged 30-70 years with a new diagnosis of primary invasive breast cancer (ICD10 C50). Eligible hospital based controls included the accompanying attendants of the women with breast cancer and patients in the general hospital without cancer. Information about diet, lifestyle, reproductive and socio-demographic factors were collected using interviewer administered structured questionnaires. Cases and controls were frequency matched on a age geography. Multivariate logistic regression models were used to estimate the odds ratio and 95% confidence intervals for the risk of breast cancer in relation to lifelong vegetarianism, following adjustment for other known risk factors for the disease.

Results

The study included 2101 cases and 2252 controls. The mean age at recruitment was similar for both cases (49.7 years) and controls (49.6 years). The mean number of children was similar for both cases (2.6) and controls (2.5) and 98% of the study population had ever breastfed. However significant differences were observed in the proportion of cases whose duration of breastfeeding was greater than six years compared to controls (22% versus 29%). Cases were significantly more likely to live in a town (23% versus 16%), have running water (84% versus 78%) and live in a permanent dwelling (88% versus 78%). The proportion of lifelong vegetarians among the cases was 29% compared to 25% amongst the controls. However, on multivariate analysis, with adjustment for known risk factors for the disease, the risk of breast cancer was the same amongst cases and controls (OR 1.01 (95% CI 0.87-1.19)).

Conclusions

The prevalence of the known reproductive and sociodemographic risk factors for breast cancer is similar in India as in other populations. To our knowledge, this is the largest study conducted in India investigating the relationship between lifelong vegetarianism and risk of breast cancer, taking into account known risk factors for the disease. These results show that lifelong exposure to a vegetarian diet does not decrease the subsequent risk of breast cancer.

Citation Format: Gathani T, Barnes I. Lifelong vegetarianism and breast cancer risk in India: A multicentre case control study of 2101 women. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-10-15.

Lifestyle and reproductive risk factors associated with anal cancer in women aged over 50 years

BACKGROUND

Anal cancer incidence increases with age and is higher in women than men. Risk factors in this group other than high-risk human papillomavirus infection are unclear.

METHODS

In all, 1.3 million women were recruited in 1996-2001 and followed for incident anal cancer. Cox regression models were used to calculate relative risks (RRs) for anal cancer by various potential risk factors.

RESULTS

Five hundred and seventeen incident anal cancers were registered over 13 years of follow-up. The largest RR was associated with a history of cervical intraepithelial neoplasia grade 3 (CIN 3; RR=4.03, 95% CI 2.59-6.28). Other factors associated with significantly increased risks in multivariate analyses were: ever smoking (RR=1.49, 1.24-1.80); previous use of oral contraceptives (RR=1.51, 1.24-1.83); nulliparity (RR=1.61, 1.24-2.07); tubal ligation (RR=1.39, 1.13-1.70) and not living with a partner (RR=1.82, 1.40-2.38). The association with smoking was significantly greater for squamous cell carcinoma than adenocarcinoma of the anus (RR 1.66 vs 0.89, P for heterogeneity=0.04).

CONCLUSIONS

History of CIN 3, smoking, past oral contraceptive use, nulliparity, tubal ligation and not living with a partner are risk factors for anal cancer in women. There was a significant increase in risk associated with smoking for squamous cell anal cancers but not adenocarcinomas.

Four New Host and Three New State Records of Dothistroma Needle Blight Caused by Dothistroma pini in the United States

During 2010 and 2011, Dothistroma needle blight (DNB), also known as red band needle blight, was observed for the first time in Cass and Pembina counties in North Dakota (ND). In Pembina Co., DNB was observed in two sites in the Jay V. Wessels Wildlife Management Area (JWWMA). In September 2009, yellow spots on green needles were observed on some trees along the western edge of one planting. By June 2010, DNB was found on third- and fourth-year needles in both JWWMA plantings. Symptoms had developed into dark brown bands or spots on necrotic needles that contained erumpent black acervuli. In June 2011, similar DNB symptoms were observed on Pinus nigra, P. flexilis, P. ponderosa, P. cembra, and P. albicaulis in the Dale E. Herman Research Arboretum, Cass Co., ND. DNB was collected in July 2011 in Brookings Co., South Dakota (SD), from a seed source provenance planting of P. ponderosa. To identify the species causing the infections, symptomatic needles were collected in 2010 from both sites in JWWMA and then again from all four locations in 2011 on all pine species infected. Needles of P. nigra from a private residence near Fairland in Shelby County, Indiana (IN), were also included in the sample set. The rDNA-ITS was PCR-amplified either directly from conidia obtained from acervuli on the needles or from cultures obtained from isolations. Amplicons were sequenced and a BLAST search was performed in GenBank. The sequences of samples obtained from P. nigra, P. flexilis, P. cembra, and P. albicaulis in ND, P. ponderosa in SD, and P. nigra from IN showed 100% sequence homology with Dothistroma pini (Accession No. AY808302). These isolates were identical to all previously assayed isolates of D. pini from Nebraska, Minnesota, and Michigan in the United States. The P. ponderosa isolates from all three sites in ND differed from the other isolates and contained a 1-bp point mutation from a C to a T at site 72 (sequence deposited in GenBank, accession KJ933441). Mating type was determined using species-specific mating type primers for D. pini (3). All 26 samples from ND and SD were of the MAT-1 idiomorph, while the sample from IN contained the MAT-2 idiomorph. All cultures are maintained at FABI, University of Pretoria, South Africa. The two species that cause DNB, D. septosporum (G. Dorog.) M. Morelet and D. pini Hulbary, are morphologically indistinguishable and molecular characterization remains essential for correct species identification (1). Host and geographical distribution range determinations of Dothistroma spp. made without molecular methods are not valid. To date, species confirmed using DNA sequences in the United States include D. septosporum in the Pacific Northwest states of Oregon and Idaho on P. ponderosa, in Montana on P. contorta v. latifolia, and D. pini in the North Central states of Nebraska, Minnesota, and Michigan on P. nigra (1). This study documents the presence of D. pini in three additional states, including a first report of DNB in ND and SD. It also includes new records of D. pini infecting P. flexilis, P. cembra, P. albicaulis, and P. ponderosa. Results of this study have expanded the documented host range of D. pini in the United States from one (P. nigra) to five species. Globally, D. pini is now known to infect a total of 10 pine hosts (2,4,5). References: (1) I. Barnes et al. Stud. Mycol. 50:551, 2004. (2) I. Barnes et al. For. Pathol. 41:361, 2011. (3) M. Groenewald et al. Phytopathology 97:825, 2007. (4) D. Piou et al. Plant Dis. 98:841, 2014. (5) B. Piskur et al. For. Pathol. 43:518, 2013.

Redefining Ceratocystis and allied genera

The genus Ceratocystis was established in 1890 and accommodates many important fungi. These include serious plant pathogens, significant insect symbionts and agents of timber degradation that result in substantial economic losses. Virtually since its type was described from sweet potatoes, the taxonomy of Ceratocystis has been confused and vigorously debated. In recent years, particulary during the last two decades, it has become very obvious that this genus includes a wide diversity of very different fungi. These have been roughly lumped together due to their similar morphological structures that have clearly evolved through convergent evolution linked to an insect-associated ecology. As has been true for many other groups of fungi, the emergence of DNA-based sequence data and associated phylogenetic inferences, have made it possible to robustly support very distinct boundaries defined by morphological characters and ecological differences. In this study, DNA-sequence data for three carefully selected gene regions (60S, LSU, MCM7) were generated for 79 species residing in the aggregate genus Ceratocystis sensu lato and these data were subjected to rigorous phylogenetic analyses. The results made it possible to distinguish seven major groups for which generic names have been chosen and descriptions either provided or emended. The emended genera included Ceratocystis sensu stricto, Chalaropsis, Endoconidiophora, Thielaviopsis, and Ambrosiella, while two new genera, Davidsoniella and Huntiella, were described. In total, 30 new combinations have been made. This major revision of the generic boundaries in the Ceratocystidaceae will simplify future treatments and work with an important group of fungi including distantly related species illogically aggregated under a single name.

Incidence of thyroid cancer in England by ethnic group, 2001-2007

BACKGROUND

Thyroid cancer incidence is increasing worldwide, but with large variations in incidence that may reflect either diagnostic bias or true ethnic differences. We sought to determine the effect of ethnicity on the incidence of thyroid cancer in England, a multiethnic population with a single health-care system.

METHODS

We analysed 11,263 thyroid cancer registrations with ethnicity obtained by linkage to the Hospital Episodes Statistics database. Incidence rate ratios (RRs) adjusted for age, sex and income were calculated for the six main non-White ethnic groups in England compared with Whites and to each other.

RESULTS

Thyroid cancer incidence was higher in all ethnic groups, except Indians, compared with Whites: in Pakistanis (RR 1.79, 99% floating confidence interval (FCI) 1.47-2.19); Bangladeshis (RR 1.99, 99% FCI 1.46-2.71); Black Africans (RR 1.69, 99% FCI 1.34-2.13); Black Caribbeans (RR 1.56, 99% FCI 1.25-1.93); and Chinese (RR 2.14, 99% FCI 1.63-2.80).

CONCLUSION

The risk of thyroid cancer in England varies significantly by ethnicity. The elevated incidence in most ethnic minorities is unlikely to be due to diagnostic bias and warrants further investigation.

Dothistroma septosporum Identified in Greece on Pinus brutia and Pinus nigra Plantations

Dothistroma needle blight (DNB) is caused by two ascomycete fungi, Dothistroma septosporum with a worldwide distribution and D. pini found in the United States, Russia, Ukraine, Hungary, and France (1). DNB has been known in Greece since the early 1980s (3) and the species responsible for the disease was reported as D. pini. In December 2011, needles were collected from three trees in Lagada, Thessaloniki regional unit of Central Macedonia (northern Greece), where the disease was first recorded. DNB infection seems to be limited to a valley in this area in Pinus nigra and P. brutia plantations established more than 50 years ago in an originally deciduous oak forest. Infections were observed over an area of 50 to 60 ha of pine plantations. Although the majority of pine trees were infected by the pathogen, the severity of the disease was relatively low and mortality of infected trees was not observed. Infections were limited to the lower branches in the 50-year-old trees, while on a limited number of younger trees of P. brutia (10 to 15 years old), infection was more severe, extending to the entire crowns of the trees. DNB does not appear to be very common in Greece. Infected needles had reddish-brown bands, usually with necrotic tips or entirely necrotic needles. Black sub-epidermal fruiting bodies (acervuli) were observed with the needle epidermis split and raised. Isolations were made from fruiting structures on needles of P. nigra and P. brutia (50-year-old trees) and P. brutia (10-year-old trees) after surface disinfection with 70% ethanol. Conidia from single fruiting bodies were transferred onto 3% malt extract agar (MEA) in petri dishes and incubated at 20°C. Colonies on MEA had a radial growth rate of 1.3 to 1.6 mm per week, were crustose, brown to grey-brown, and partly covered with slimy masses of conidia. The agar surrounding the colonies had a reddish color. Conidia from acervuli on the needles and the cultures were similar in shape and size, filiform, hyaline, 2 to 4 septate, and 1.8 to 2.5 (3.3) × 22 to 47 μm long. DNA was extracted from three cultures: one from P. nigra (CMW 37966) and two from P. brutia (CMW 37965, CMW 37967) using a standard phenol/chloroform method. The internal transcribed spacer (ITS) region was amplified and sequenced (1). Sequences were 100% identical to D. septosporum isolates in GenBank (e.g., AY808291). In addition, up to 12 randomly selected acervuli were excised directly from the needles of each of the three trees and DNA was extracted using PrepMan solution (Applied Biosystems). The mating types of these samples were determined using species-specific mating type primers for D. pini and D. septosporum (2). All acervuli were confirmed to be those of D. septosporum. Both mating types were found on needles from P. brutia and P. nigra. However, the teleomorph of D. septosporum was not detected on infected needles. References: (1) I. Barnes et al. For. Pathol. 41:361, 2011. (2) M. Groenewald et al. Phytopathology 97:825, 2007. (3) D. S. Kailidis and S. Markalas. Dasika Chronika 24:257, 1981 (in Greek).

FT-IR product study of the reactions of NO3 radicals with ortho-, meta-, and para-cresol

Product analyses of the NO3 radical-initiated oxidation of ortho-, meta-, and para-cresol have been performed in large-volume chamber systems at the University of Wuppertal (1080 L quartz glass reactor: QUAREC) and the European Photoreactor (EUPHORE), Valencia, Spain. The reaction of O3 with NO2 was used for the in situ generation of NO3 radicals in both QUAREC and EUPHORE. In the QUAREC experiments the gas-phase reaction of ortho-cresol isomer with NO3 yielded (11.5 ± 0.8) % 6-methyl-2-nitrophenol (6M2NP), (4.4 ± 0.3) % methyl-1,4-benzoquinone (MQUIN) and (77.2 ± 6.3) % HNO3. The reaction of NO3 radicals with meta-cresol yielded (21.2 ± 1.4) % 3-methyl-2-nitrophenol (3M2NP), (22.8 ± 1.8) % 3-methyl-4-nitrophenol (3M4NP), (23.5 ± 1.8) % 5-methyl-2-nitrophenol (5M2NP), (4.2 ± 0.7) % MQUIN and (72.3 ± 6.4) % HNO3. In the reaction of NO3 radicals with para-cresol, 4-methyl-2-nitrophenol (4M2NP) and HNO3 were identified as products with yields of (41.3 ± 3.7) % and (85.0 ± 10.2) %, respectively. In the EUPHORE chamber not all products were formed at levels above the detection limit, however, in cases where detection was possible similar product yields were observed. The product formation yields determined in both chambers are compared with available literature data and a gas-phase mechanism is proposed to explain the formation of the products observed from the reaction of NO3 and with cresol isomers.

Geochemical evidence of present-day serpentinization

Ultrabasic (pH > 11) water issues from some fresh ultramafic bodies. The properties of the ultrabasic solutions are believed to be due to current reactions yielding serpentine from primary olivines and pyroxenes. The low concentrations of divalent airon. divalent magnesium, and dissolved silica from the serpentinization require an increase in rock volume.

Atmospheric photooxidation of fluoroacetates as a source of fluorocarboxylic acids

A 1080 L environmental chamber with in situ FTIR spectroscopy detection was used to study the product distribution and the mechanism of the Cl-initiated photooxidation of a series of fluoroacetates. The gas-phase reactions of Cl atoms with ethyl trifluoroacetate (CF(3)C(O)OCH(2)CH(3)), methyl trifluoroacetate (CF(3)C(O)OCH(3)), and methyl difluoroacetate (CF(2)HC(O)OCH(3)) were investigated at 296 +/- 2 K and atmospheric pressure (approximately 760 Torr) of synthetic air. The fate of the fluoroalkoxy radicals formed in the reaction with Cl atoms mainly occurs through (i) an H-atom abstraction by reaction with O(2,) to produce the corresponding fluoroanhydride and (ii) an alpha-ester rearrangement via a five-membered ring intermediate to give the corresponding fluoroacetic acid. The yields of fluoroacids (CF(2)XC(O)OH, with X = H, F) obtained were as follows: 78 +/- 5, 23 +/- 2, and 30 +/- 5% for CF(3)C(O)OCH(2)CH(3), CF(3)C(O)OCH(3), and CF(2)HC(O)OCH(3,), respectively. Yields of <or=20, <or= 80, and <or=55% have been estimated for the anhydride formation from CF(3)C(O)OCH(2)CH(3), CF(3)C(O)OCH(3), and CF(2)HC(O)OCH(3), respectively. Formation of CF(2)O, with yield of 13 +/- 2% has been observed for the reaction of Cl with CF(2)HC(O)OCH(3). The measured yields are rationalized in terms of mechanisms consisting of competitive reaction channels for the radicals formed in the oxidation, that is, reaction with O(2), alpha-ester rearrangement and a decomposition pathway. The stability of the five-membered transition state of the alpha-ester rearrangement is correlated with the acid yields observed for the different fluoroacetates. Atmospheric implications, especially with regard to the fluorocarboxylic acid formation, are discussed.

Development and characterization of polymorphic markers for the sap-stain fungus Ophiostoma quercus

Eight polymorphic markers were developed from South African isolates of Ophiostoma quercus. The genome was screened for repeat regions using the fast isolation by amplified fragment length polymorphism of sequences containing repeats protocol and 20 de novo primer pairs flanking putative microsatellite regions were designed. Eight loci were optimized and their polymorphisms evaluated by sequencing. The repeat and flanking regions were highly polymorphic containing both indels and base-pair substitutions revealing a total of 46 alleles in 14 isolates and an average heterozygosity of 0.68. Substantial sequence variability makes these markers useful for genotyping populations in order to calculate diversity and monitor global movement of O. quercus.

Reaction of Cl Atoms with C6F13CH2OH, C6F13CHO, and C3F7CHO

The Cl atom initiated oxidation of C(6)F(13)CH(2)OH, C(6)F(13)CHO, and C(3)F(7)CHO was investigated at 298 K and 1000 mbar pressure of air in a photoreactor using in situ Fourier transform infrared (FTIR) analysis. The rate coefficient for the reaction Cl + C(6)F(13)CH(2)OH (reaction 2) was measured using a relative method: k(2) = (6.5 +/- 0.8) x 10(-13) cm(3) molecule(-1) s(-1). C(6)F(13)CHO was detected as the major primary product, while CO and CF(2)O were found to be the major secondary products. A fitting procedure applied to the concentration-time profiles of C(6)F(13)CHO provided a production yield of (1.0 +/- 0.2) for this aldehyde in reaction 2, and the rate coefficient for the reaction Cl + C(6)F(13)CHO (reaction 4) was k(4) = (2.8 +/- 0.7) x 10(-12) cm(3) molecule(-1) s(-1). A high CO yield observed in the oxidation of C(6)F(13)CH(2)OH, (52 +/- 1)%, is attributed to the Cl atom initiated oxidation of C(6)F(13)CHO. High CO yields, (61 +/- 2)% and (85 +/- 5)%, were also measured in the Cl atom initiated oxidation of C(3)F(7)CHO in air and nitrogen, respectively. These high CO yields suggest the occurrence of a decomposition reaction of the perfluoroacyl, C(6)F(13)CO, and C(3)F(7)CO radicals to form CO which will compete with the combination reaction of these radicals with oxygen to form perfluoroacyl peroxy radicals in the presence of air. The latter radicals C(n)F(2)(n)(+1)CO(O)(2) (n = 6-12), through their reaction with HO(2) radicals, are currently considered as a possible source of persistent perfluorocarboxylic acids which have been detected in the environment. The consequences of the present results would be a reduction of the strength of this potential source of carboxylic acids in the atmosphere.

The phylogenetic position of the ‘giant deer’ Megaloceros giganteus

The giant deer, or 'Irish elk', has featured extensively in debates on adaptation, sexual selection, and extinction. Its huge antlers--the largest of any deer species, living or extinct--formed a focus of much past work. Yet the phylogenetic position of the giant deer has remained an enigma. On the basis of its flattened antlers, the species was previously regarded as closely related to the living fallow deer. Recent morphological studies, however, have challenged that view and placed the giant deer closer to the living red deer or wapiti. Here we present a new phylogenetic analysis encompassing morphological and DNA sequence evidence, and find that both sets of data independently support a sister-group relationship of giant and fallow deer. Our results include the successful extraction and sequencing of DNA from this extinct species, and highlight the value of a joint molecular and morphological approach.

Ceratocystis pirilliformis, a new species from Eucalyptus nitens in Australia

Several species of Ceratocystis have been recorded on Eucalyptus. These include C. fimbriata, C. eucalypti, C. moniliformis and C. moniliformopsis. Of these, only C. fimbriata is known as a pathogen; it recently has been found causing serious wilt diseases in Uganda, Congo and Brazil. This study was undertaken to collect Ceratocystis species, including C. eucalypti, from artificially induced wounds on Eucalyptus nitens near Canberra in southeastern Australia. Trees were wounded in October 2000, and wounds were examined approximately one month later. Ascomata characteristic of a Ceratocystis species were found covering the wounds, and this fungus also was isolated from the wood using carrot baiting. This species of Ceratocystis has hat-shaped ascospores similar to those of C. fimbriata, but it differs from C. fimbriata and all other species of Ceratocystis in that it possesses ascomata with a pyriform base. Comparison of DNA sequences from the ITS and 5.8S rRNA operon confirmed that the fungus from E. nitens in Australia is unique, and we describe it here as a new species, C. pirilliformis.

Agreement between general practice prescription data and self-reported use of hormone replacement therapy and treatment for various illnesses

BACKGROUND

Epidemiological studies of the effects of hormone replacement therapy (HRT) often rely on exposure data and information on past health from self-administered questionnaires. The accuracy with which women report current use of HRT and the specific preparation in use is not known. This study aims to compare aspects of self-reported use of HRT and treatment for various conditions with data from general practice prescription records.

METHODS

Reported questionnaire data on use of HRT were compared with those on the general practice prescription record for 570 women participating in the Million Women Study from two general practices in the UK.

RESULTS

There was excellent agreement between data from the self-administered questionnaire and the prescription record: 96% agreement (kappa = 0.91) for current use of HRT, 95% agreement (kappa = 0.90) for any use of HRT during the period covered by the prescription record, and 97% agreement (kappa = 0.95) among current users for whether the HRT preparation contained oestrogen alone, combined oestrogen/progestogen, or some other constituents. Among former HRT users who provided questionnaire information on the preparation they used most recently, there was 69% agreement on the proprietary preparation used and 97% agreement (kappa = 0.93) on the hormonal constituents used. Agreement between reported treatment for various conditions and the presence of a prescription appropriate for that condition ranged from 89-99% (kappa 0.53-0.92), and was highest for thyroid disease and asthma.

CONCLUSION

Important aspects of use of HRT, such as type of preparation currently being used, are reported very reliably by women completing a self-administered questionnaire.

Endogenous sex hormones and breast cancer in postmenopausal women: reanalysis of nine prospective studies

BACKGROUND

Reproductive and hormonal factors are involved in the etiology of breast cancer, but there are only a few prospective studies on endogenous sex hormone levels and breast cancer risk. We reanalyzed the worldwide data from prospective studies to examine the relationship between the levels of endogenous sex hormones and breast cancer risk in postmenopausal women.

METHODS

We analyzed the individual data from nine prospective studies on 663 women who developed breast cancer and 1765 women who did not. None of the women was taking exogenous sex hormones when their blood was collected to determine hormone levels. The relative risks (RRs) for breast cancer associated with increasing hormone concentrations were estimated by conditional logistic regression on case-control sets matched within each study. Linear trends and heterogeneity of RRs were assessed by two-sided tests or chi-square tests, as appropriate.

RESULTS

The risk for breast cancer increased statistically significantly with increasing concentrations of all sex hormones examined: total estradiol, free estradiol, non-sex hormone-binding globulin (SHBG)-bound estradiol (which comprises free and albumin-bound estradiol), estrone, estrone sulfate, androstenedione, dehydroepiandrosterone, dehydroepiandrosterone sulfate, and testosterone. The RRs for women with increasing quintiles of estradiol concentrations, relative to the lowest quintile, were 1.42 (95% confidence interval [CI] = 1.04 to 1.95), 1.21 (95% CI = 0.89 to 1.66), 1.80 (95% CI = 1.33 to 2.43), and 2.00 (95% CI = 1.47 to 2.71; P(trend)<.001); the RRs for women with increasing quintiles of free estradiol were 1.38 (95% CI = 0.94 to 2.03), 1.84 (95% CI = 1.24 to 2.74), 2.24 (95% CI = 1.53 to 3.27), and 2.58 (95% CI = 1.76 to 3.78; P(trend)<.001). The magnitudes of risk associated with the other estrogens and with the androgens were similar. SHBG was associated with a decrease in breast cancer risk (P(trend) =.041). The increases in risk associated with increased levels of all sex hormones remained after subjects who were diagnosed with breast cancer within 2 years of blood collection were excluded from the analysis.

CONCLUSION

Levels of endogenous sex hormones are strongly associated with breast cancer risk in postmenopausal women.

Dynamics of Pleistocene population extinctions in Beringian brown bears

The climatic and environmental changes associated with the last glaciation (90,000 to 10,000 years before the present; 90 to 10 ka B.P.) are an important example of the effects of global climate change on biological diversity. These effects were particularly marked in Beringia (northeastern Siberia, northwestern North America, and the exposed Bering Strait) during the late Pleistocene. To investigate the evolutionary impact of these events, we studied genetic change in the brown bear, Ursus arctos, in eastern Beringia over the past 60,000 years using DNA preserved in permafrost remains. A marked degree of genetic structure is observed in populations throughout this period despite local extinctions, reinvasions, and potential interspecies competition with the short-faced bear, Arctodus simus. The major phylogeographic changes occurred 35 to 21 ka B.P., before the glacial maximum, and little change is observed after this time. Late Pleistocene histories of mammalian taxa may be more complex than those that might be inferred from the fossil record or contemporary DNA sequences alone.

Microsatellite markers reflect intra-specific relationships between isolates of the vascular wilt pathogen Ceratocystis fimbriata

summary Ceratocystis fimbriata is a serious wilt and canker stain pathogen with a wide geographical distribution and host range that includes both woody and herbaceous plants. Previous studies using hybridization have shown that isolates of C. fimbriata from different hosts and origins differ in colony morphology, pathogenicity and growth rate, as well as conidial state. It has therefore been suggested that distinct strains, linked to host or geographical origin, are encompassed in C. fimbriata. The aim of this study was to develop PCR-based microsatellite markers for population studies on C. fimbriata. ISSR-PCR was used to target specific microsatellite regions of DNA from C. fimbriata. These amplified products were cloned and sequenced. Primer pairs were designed from these sequences to flank the microsatellite regions. From 24 primer pairs, 11 polymorphic primers were selected and tested on a number of C. fimbriata isolates representing a wide host and geographical range. Cluster analyses of the results indicate that these markers clearly distinguish between different geographical and host specific populations of C. fimbriata. The results are concordant with sequence data from the internal transcribed spacer (ITS) region of the rDNA operon of the same isolates. These markers will be useful in future studies of C. fimbriata population structure and diversity.

A molecular analysis of dietary diversity for three archaic Native Americans

DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2-4 different animal species and 4-8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.

Organic aerosol formation during the atmospheric degradation of toluene

Organic aerosol formation during the atmospheric oxidation of toluene was investigated using smog chamber systems. Toluene oxidation was initiated by the UV irradiation of either toluene/air/NOx or toluene/air/CH3ONO/NO mixtures. Aerosol formation was monitored using scanning mobility particle sizers and toluene loss was monitored by in-situ FTIR spectroscopy or GC-FID techniques. The experimental results show that the reaction of OH radicals, NO3 radicals and/or ozone with the first generation products of toluene oxidation are sources of organic aerosol during the atmospheric oxidation of toluene. The aerosol results fall into two groups, aerosol formed in the absence and presence of ozone. An analytical expression for aerosol formation is developed and values are obtained for the yield of the aerosol species. In the absence of ozone the aerosol yield, defined as aerosol formed per unit toluene consumed once a threshold for aerosol formation has been exceeded, is 0.075 +/- 0.004. In the presence of ozone the aerosol yield is 0.108 +/- 0.004. This work provides experimental evidence and a simple theory confirming the formation of aerosol from secondary reactions.